Arabidopsis thaliana vs Olea europaea var. sylvestris LastZ results
Arabidopsis thaliana (Arabidopsis thaliana, TAIR10) and Olea europaea var. sylvestris (Olea europaea var. sylvestris, O_europaea_v1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Plants release 100. Arabidopsis thaliana was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.
Configuration parameters
Parameter | Value |
---|---|
Gap open penalty (O) | 400 |
Gap extend penalty (E) | 30 |
HSP threshold (K) | |
Threshold for gapped extension (L) | 3000 |
Threshold for alignments between gapped alignment blocks (H) | 2200 |
Masking count (M) | |
Seed and Transition value (T) | 1 |
Scoring matrix (Q) | Default: A C G T 91 -114 -31 -123 -114 100 -125 -31 -31 -125 100 -114 -123 -31 -114 91 |
Chunking parameters
Parameter | Arabidopsis thaliana | Olea europaea var. sylvestris |
---|---|---|
Chunk size | 10,000,000 | 10,100,000 |
Overlap | 0 | 100,000 |
Group set size | 0 | 10,100,000 |
Masking options |
Statistics over 210,672 alignment blocks
Genome coverage (bp) | Coding exon coverage (bp) | |
---|---|---|
Arabidopsis thaliana |
Uncovered: 81,212,045 out of 119,667,750 |
Uncovered: 8,980,949 out of 33,775,569 |
Olea europaea var. sylvestris |
Uncovered: 1,076,944,662 out of 1,140,989,389 |
Uncovered: 22,364,326 out of 52,755,300 |
Block size distribution
Size range | All 210,672 alignment blocks | Blocks grouped in nets | |||
---|---|---|---|---|---|
# blocks | Total size (incl. gaps) | # nets | Total size (incl. gaps) | ||
1 bp - 10 bp | 1,717 |
9.1 kb |
|||
10 bp - 100 bp | 33,024 |
2.3 Mb |
10,168 |
725.8 kb |
|
100 bp - 1 kb | 161,798 |
53.6 Mb |
55,116 |
21.0 Mb |
|
1 kb - 10 kb | 14,049 |
24.4 Mb |
25,444 |
56.2 Mb |
|
10 kb - 100 kb | 84 |
1.2 Mb |
252 |
3.5 Mb |